In our first IndieBio SF class we'll have Sensa.io joining us, Greg (who worked out of Biocurious, Counter Culture Labs and most recently Genspace) and the team are really passionate about building an open source bioreactor (they've build several bioreactors previously) and we're really pleased to be able to back him through IndieBio SF. I'm sure he'd welcome your thoughts and help with the open source bioreactor they'll be building to ensure it's as useful as possible to the community!

have you seen this Multiplex Automated Genome Engineering (MAGE) project http://wyss.harvard.edu/viewpage/330/

every thing is possible once you have decided to do it ... so keep doing the good work.. tell me more about what you know

about factor VIII ...

and always remember one thing no matter what they say ...

"Positive anything is better than negative nothing."

On Sunday, February 1, 2015 at 1:22:54 AM UTC+5:30, Simon Rose wrote:

Hi everyone I'm interested in making a synthetic pathogen sensor using human toll- like receptors 2 and 6 The idea is to ligate the pathogen-sensing, extracellular domains of each TLR (or possibly just the recognition module, consisting of just a single residue) to one half of a GFP, producing a visible signal when the TLRs dimerise. Using a prokaryotic chassis to carry the TLRs might not be possible owing to the absence of endoplasmic reticula in prokaryotes, and the consequent problems with protein folding, as well as with being able to anchor the transmembrane domains of the TLRs in the cell wall. Any TLRs expressed might not fold properly. I think that TLR signal transduction is not well understood hence the use of GFPs as reporters, as bacteria would lack the requisite intracellular signalling pathways. If these problems prove insuperable, then a eukaryotic chassis might have to be used. Anyway, it's a learning curve!

There is also Magic Lantern that adds features to the software in the camera. It is FOSS. If is is anything like CHDK (for the PowerShot cameras), it would give you the ability to run programs inside the camera itself. If not, you could add that capability.

thanks to JT first for his amazing project and sharing it as well as the content around it. Just to compelete this thread here a few links of more turbidostat and chemostat systems that were built by the Dunham and the Klavin lab:

I am currently planning to built a low cost model of the Evolinator and optionally combing it with another vessel. We will see :). However, I intend to culture anaerob archeae that grow really slow (doubling time 4h) so I will start with the normal Evolvinator set up under a DIY anaerobic chamber. Does anybody has experience with anaerobes? Are they suitable for such an automated culturing endeavor?

Cheers and thanks for feedback

Johann

Am Freitag, 28. Oktober 2011 04:19:41 UTC+2 schrieb Jt:

Hello,

New to the DIYBio group.

I have created a turbidostat that I would like to share with the community. In brief, it uses an Arduino to control a peristaltic pump based on OD readings, includes temperature control as well as an aquarium pump for aeration. Additionally, I have a version that forgoes the pump and relies on air pressure and valves to move fluid through the system. The system currently uses the Arduino Ethernet Shield and HTML interface to control it, though an interface over serial could be easily written for anyone who wants to go into the code.

Besides the Arduino code, I have CAD drawings for the housings, EAGLE .brd and .sch files for the additional "Turbidostat Shield" I made that contains the electrical components, as well as the parts list. I haven't created the How-To yet because I'm not sure where the best place to publish the designs are and what the demand is from the community. I read that there was an open source turbidostat project on DIYbio, but cannot find its current progress.

In any case, the device is relatively cheap (especially depending on what you have on hand and where you want to cut corners), and I think it would be helpful the community.

thanks again for sharing your amazing project and also linking to the other turbidostats and chemostat systems from the dunham and kalvin lab. You mentioned in your Evolvinator that for anaerobic samples one could just flush the system with an anoxic gas. I don't think this will work especially working with oxygen atolerant anaerobes. I was thinking about building your system under a diy anaerobic chamber (there are lot of diy projects for those out).

Do you have any idea, papers, literature that could help me in cultivating Archeae in turbidostat system (does it make sense with an doubling time of 4h) ? Also for your problem with the formation of biofilms : there has been a patent out to solve that. They seem to use a combination of two culture vessels - changing vessels frequently to kill of biofilm producers and dilution resistant strains. Since you used yout system at Ginko Bioworks you can not really use it for commercial interest as it is patented but mabe there is a clever design around.

I think a DIY turbidostat - especially one that enables growing bugs for thousands of generation - would be powerful in changing substrate affinities and cleaning up waste streams.On Friday, October 28, 2011 at 5:13:03 PM UTC+2, Jt wrote:

Awesome. Thank you Cathal, Jonathan, and John.

openwetware and github seem like the right combination.

To give a full story, I work for Ginkgo BioWorks and have developed this device for our own inhouse bug testing/polishing. Though the current iteration is probably a little more sophisticated than a lot of hobbyists would want to get into, there are pared down versions which are totally within grasp. We don't have any intention of selling the device so we want to open source it to kick start all the diy bioers out there. So I don't know if I'll go through the lengths of making it Sparkfun/Ponoko purchasable myself, but take Jonathan's advice of setting it free. Also, a UBW is most definitely in the works, which I am happy to share as well.

Look forward to the openwetware How-To and please continue posting any suggestions you have!

jt

Also to respond to your question Cathal: a IR LED and photodiode pair work perfectly well to measure OD and can be more accurate than a lot of common laboratory cuvette readers, especially if you can get the optics down (super cheap too).

Hi everyone I'm interested in making a synthetic pathogen sensor using human toll- like receptors 2 and 6 The idea is to ligate the pathogen-sensing, extracellular domains of each TLR (or possibly just the recognition module, consisting of just a single residue) to one half of a GFP, producing a visible signal when the TLRs dimerise. Using a prokaryotic chassis to carry the TLRs might not be possible owing to the absence of endoplasmic reticula in prokaryotes, and the consequent problems with protein folding, as well as with being able to anchor the transmembrane domains of the TLRs in the cell wall. Any TLRs expressed might not fold properly. I think that TLR signal transduction is not well understood hence the use of GFPs as reporters, as bacteria would lack the requisite intracellular signalling pathways. If these problems prove insuperable, then a eukaryotic chassis might have to be used. Anyway, it's a learning curve!

ps, I won't be doing this in a biohacklab but in a university lab under supervision. I've just seen the post about recombinant factor 8 by the way. Sterile techniques, if required should be no problem

On Saturday, January 31, 2015 at 7:52:54 PM UTC, Simon Rose wrote:

Hi everyone I'm interested in making a synthetic pathogen sensor using human toll- like receptors 2 and 6 The idea is to ligate the pathogen-sensing, extracellular domains of each TLR (or possibly just the recognition module, consisting of just a single residue) to one half of a GFP, producing a visible signal when the TLRs dimerise. Using a prokaryotic chassis to carry the TLRs might not be possible owing to the absence of endoplasmic reticula in prokaryotes, and the consequent problems with protein folding, as well as with being able to anchor the transmembrane domains of the TLRs in the cell wall. Any TLRs expressed might not fold properly. I think that TLR signal transduction is not well understood hence the use of GFPs as reporters, as bacteria would lack the requisite intracellular signalling pathways. If these problems prove insuperable, then a eukaryotic chassis might have to be used. Anyway, it's a learning curve!

Hi everyone I'm interested in making a synthetic pathogen sensor using human toll- like receptors 2 and 6 The idea is to ligate the pathogen-sensing, extracellular domains of each TLR (or possibly just the recognition module, consisting of just a single residue) to one half of a GFP, producing a visible signal when the TLRs dimerise. Using a prokaryotic chassis to carry the TLRs might not be possible owing to the absence of endoplasmic reticula in prokaryotes, and the consequent problems with protein folding, as well as with being able to anchor the transmembrane domains of the TLRs in the cell wall. Any TLRs expressed might not fold properly. I think that TLR signal transduction is not well understood hence the use of GFPs as reporters, as bacteria would lack the requisite intracellular signalling pathways. If these problems prove insuperable, then a eukaryotic chassis might have to be used. Anyway, it's a learning curve!

This argument would hold more water for me if there weren't already a
multi-billion voluntarily labelled and anti-GMO market: Organic food.
And plenty of people who subscribe to it entirely, creating a control group.

All of which is irrelevant, because GE foods are already extensively tested.

The "control group" in this case is also anti-everything, including
vaccines and antibiotics, and are currently suffering from a serious
measles problem. The confounding factors involved in treating nutters as
a "natural experiment" are significant and difficult to account for.
They're also fond of letting unlicensed people jab them with hot
needles, realign their spinal column, and feed them dilute "mystery
medicine" or mercury-laced ayurveda, so you really can't tell if a
difference between groups is due to your chosen factor or something else.

Maybe this is radical of me to suggest, but there's this thing called
the "scientific method" which is fairly good at establishing whether
stuff is safe or not, and applying it in this case might be a good
approach. Oh wait, people have. Extensively. Repeatedly. Ad nauseum.

The software might be nice, but the Canon has higher resolution, lower noise, higher video speeds, and a larger sensor.

That won't matter if all you need is 50 micron (or even 1 micron) resolution. But I've been getting close to 0.2 micron resolution using a Canon T3i (a fairly old camera) and a homemade microscope (I also use an excellent phase-contrast research microscope and get similar resolution but with much less aberration).

When controlled by my computer, I find the Canon to be quite suited to microphotography. You look at the computer monitor, and click on the shutter icon to take the picture. It's pretty friendly.

I was telling Nathan how flex circuits like are used in LCD screens for desktops of a few years ago are a commodity process of making layers with 50 micron width and space between and might be repurposed to fabbing microfluidics inexpensively. I took a flatbed scanner photo of the flex circuit that could not get down to its resolution, and emailed that, and offered to send him a piece to look at under a microscope, since I did not have any good digital camera for microscope photos.

I was saying how I'd take the lens off of a Canon powershot for that, but it still has a crummy user interface for microphotography, which triggered him telling me about this:

It's got a perfect user interface for microphotography -- python programmed machine vision programs that can recognize features in a scene. Just add a little problem-specific development and you have a cell counter program. Well, add that not-yet-existing, accurate and inexpensive plastic molded microgrid to drop on your samples then top with a cover slip, *then* hit the go button of the counting program...

On 01/31/2015 08:08 AM, Sunil Phani wrote:
> nothing to get alarmed about mammalian cell culture until it's being used up on human beings ...

It's just that "it" could be used on YOU accidentally as you do lab technique...
and then consider side effects of disease spread risk from your lab cultures, etc.

So, "study up" is all they are saying.

I don't think anyone was alarmed. But...

They care about you even though they don't know you.

They worry when you say non-chalantly, "nothing to get alarmed about mammalian cell culture"...

They worry comparing your non-spell checked emails to all the long sequences of exacting detail
needed to do mammalian cell culture, and worry that "It might not work out..." as Bob Allen,
a good horse trainer says fairly often to his students...